Results 71 to 80 of about 439,865 (314)

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

BMC Research Notes, 2018
Objective The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants).
Thomas Sauvage, Sophie Plouviez, William E. Schmidt, Suzanne Fredericq   +3 more
doaj   +1 more source

Lineage tree analysis of immunoglobulin variable-region gene mutations in autoimmune diseases: chronic activation, normal selection [PDF]

, 2006
Autoimmune diseases show high diversity in the affected organs, clinical manifestations and disease dynamics. Yet they all share common features, such as the ectopic germinal centers found in many affected tissues.
Neta S. Zuckerman, Zuckerman, N.S., Michal Barak, Roshini S. Abraham, Ramit Mehr, Mehr, Ramit, Steiman-Shimony, Avital, David I. Stott, Edelman, H., Hutzler, A., Edelman, Hanna, Zuckerman, Neta S., Stott, David I., Shahaf, G., Deborah Dunn-Walters, Abraham, Roshim S., Shahaf, Gitit, Stott, D.I., Gitit Shahaf, Dunn-Walters, D., Avital Steiman-Shimony, Hutzler, Anat, Barak, M., Steiman-Shimony, A., Barak, Michal, Mehr, R., Dunn-Walters, Deborah, Anat Hutzler, Hanna Edelman, Abraham, R.S.   +29 more
core   +1 more source

Decreased cold‐sensing function of the transient receptor potential channel TRPM8 from tailed amphibians

FEBS Open Bio, EarlyView.
Despite frogs avoiding low temperatures, examination of four salamander species revealed that none avoided cold and all possessed cold tolerance. Functional analysis of TRPM8, a cold sensor, showed that all salamander TRPM8s had lost their cold sensitivity.
Tadahiro Sawao, Daiki Kobayashi, Shogo Hori, Osamu Saitoh   +3 more
wiley   +1 more source

GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution

BMC Genomics, 2018
Background Several methods have been developed for the accurate reconstruction of gene trees. Some of them use reconciliation with a species tree to correct, a posteriori, errors in gene trees inferred from multiple sequence alignments. Unfortunately the
Emmanuel Noutahi, Nadia El-Mabrouk
doaj   +1 more source

Evolutionarily divergent DUF4465 domains have a common vitamin B12‐binding function

FEBS Open Bio, EarlyView.
We show that DUF4465 family proteins, widespread across bacteria from gut microbiomes, hydrothermal vents, and soil, share a common vitamin B12‐binding function. These augmented β‐jellyroll proteins bind vitamin B12 via extended loops. Our findings establish sequence‐diverse DUF4465 proteins as a widespread class of B12‐binding proteins, highlighting ...
Charlea Clarke, Michal Banasik, Rokas Juodeikis, Martin J. Warren, Richard W. Pickersgill   +4 more
wiley   +1 more source

PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.

PLoS ONE, 2012
Both multiple sequence alignment and phylogenetic analysis are problematic in the "twilight zone" of sequence similarity (≤ 25% amino acid identity). Herein we explore the accuracy of phylogenetic inference at extreme sequence divergence using a variety ...
Gaurav Bhardwaj, Kyung Dae Ko, Yoojin Hong, Zhenhai Zhang, Ngai Lam Ho, Sree V Chintapalli, Lindsay A Kline, Matthew Gotlin, David Nicholas Hartranft, Morgen E Patterson, Foram Dave, Evan J Smith, Edward C Holmes, Randen L Patterson, Damian B van Rossum   +14 more
doaj   +1 more source

Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications

Frontiers in Bioengineering and Biotechnology, 2021
Large enzyme families such as the groups of zinc-dependent alcohol dehydrogenases (ADHs), long chain alcohol oxidases (AOxs) or amine dehydrogenases (AmDHs) with, sometimes, more than one million sequences in the non-redundant protein database and ...
Fernanda L. Sirota, Sebastian Maurer-Stroh, Sebastian Maurer-Stroh, Zhi Li, Frank Eisenhaber, Frank Eisenhaber, Frank Eisenhaber, Birgit Eisenhaber, Birgit Eisenhaber   +8 more
doaj   +1 more source

Multiple sequence alignment with the Divide-and-Conquer method.

, 1998
Stoye J. Multiple sequence alignment with the Divide-and-Conquer method. Gene. 1998;211(2):GC45-GC56.An improved algorithm for the simultaneous alignment of multiple protein and nucleic acid sequences, the Divide-and-Conquer Alignment procedure (DCA), is
Jens Stoye, Stoye, Jens ; https://orcid.org/   +1 more
core   +1 more source

Long‐term hippocampal alterations and cognitive impairment in a murine model of surgical sepsis

FEBS Open Bio, EarlyView.
Using a mouse model of surgical sepsis, we tested long‐term memory and analyzed the transcriptome of single cells isolated from the hippocampus. Survivor mice showed worse memory, loss of certain brain cell subpopulations, and abnormal immune cell activity—suggesting that post‐sepsis brain alterations may be linked to cognitive deficits.
Dong Seong Cho, Rebecca Schmitt, Aneesha Dasgupta, Alexandra Ducharme, Jason Doles   +4 more
wiley   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source